Hey everyone,
Someone has given me a monkey volume (it's actually the average of 4 volumes and the gray-white matter contrast is pretty good) and I need to make a surface from it. I've never dealt with non-human datasets, but I did read in the freesurfer mailing archives that control points must always be added to a monkey T1 volume in order to get a decent wm segmentation. I ran recon-all stage1 and I got a first pass surface, and indeed I need to add control points because there is alot of white matter in the frontal lobes that is not being included in the segmentation. So I selected some control points (in the T1 volume, within the white matter), and then I ran this command: recon-all stage1 -usecontrolpoints -subjid monkey_surf
I looked at the output and it doesn't seem to have helped at all. The segmentation still doesn't include the wm where the control points were added. What am I doing wrong? I've attached a jpg file to illustrate my problem.
Thanks, Peggy
